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Sho Takamatsu, a sixth grader, proceeds to school following a bitter argument with his mother about her throwing out his things. But as Sho attends his class, a tremor suddenly shakes the facility, and the students and faculty find that the school has somehow been transported into a wasteland. In time, they find others wandering through the strange landscape, lost. One of them, a three-year-old boy named Yu, shows Sho a memorial buried in the dust which commemorates the disappearance of their school - indicating that they somehow have landed in the future. As it later turns out, the world succumbed to a variety of environmental disasters some time after the school was time-warped, leaving the Earth nearly depopulated at the end of the 20th century.

In the face of this unexpected and frightening development, many of the adults and students at school lose their wits. One of the teachers, Wakahara, goes completely insane and murders his colleagues and some of the students before he is killed by Sho in self-defense, while the previously mild-mannered food delivery man for the school, Sekiya, puts his own survival before the children's lives, which leaves the children with no adult guidance. In this desperate situation, Sho attempts to take charge in order to ensure the survival of all. He meets Nishi, a fifth-grader from Nagao, who has the mysterious psychic power to reach into the past. When Sho's mother, who is remorseful over her son's disappearance, is contacted by Sho through Nishi's power in times of great need, she goes great lengths to assist her son by preparing things in her own time so that they might help Sho in this bleak future.

The stranded children meet many challenges in their desperate fight for survival. They encounter hostile monsters which claim the lives of several children. They are also affected by a deadly plague, the growing shortage of food and water, hostile delinquents who sow dissension amongst the students and threaten inner stability, and most of all, creeping madness. Sho and his closest companions, who form the school's "government", fight a fierce struggle but are unable to save many of their comrades, who keep falling prey to the myriad of dangers around them and their own despair. In the end, Nishi falls into a coma but the students are nevertheless able to use her powers as a medium between the children and Sho's mother. Sho's mother sends a rocket ship full of supplies to the children. Due to a series of mishaps, only little Yu is able to return, delivering Sho's journal to Sho's mother. However, in the future the children happen upon several beneficial factors which promise the return of life to the devastated Earth and their own survival, and they resolve to stay and try to rebuild the world from the ashes of the past.